systemdf: Wrapper of system calls in which input and output are all...

In jokergoo/epik: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Description

Wrapper of system calls in which input and output are all table-like files

Usage

systemdf(cmd, envir = parent.frame(), verbose = FALSE)

Arguments

cmd	shell command
envir	environment where to look for variables encoded in cmd
verbose	whether print messages

Details

This function (system + data frame) provides a convinient way to invoke system calls in R. Since most of system calls expect tables as inputs and outputs, systemdf() does following step by step:

• use backtick to mark variables which are data frames or other variables which can be converted to data frames by as.data.frame

• extract the variable names and look for data frames in envir

• write data frames into temporary files

• replace variables names with paths that correspond to temporary files

• make the system call

• finally send back the output by piping back to R

A simple example is as follows:

  bed1 = circlize::generateRandomBed(nr = 1000)
  bed2 = circlize::generateRandomBed(nr = 1000)
  df = systemdf("bedtools closest -a `bed1` -b `bed2` | awk '$1==\"chr1\"'")  

Value

A data frame. Column names may be lost.

Author(s)

Zuguang Gu <[e-mail]>

Examples

if(Sys.info()["sysname"] %in% c("Linux", "Darwin")) {
    df = data.frame(x = sample(1:10, 10), y = sample(11:20, 10))
    systemdf("sort -k1,1n `df`")
}

jokergoo/epik documentation built on Sept. 28, 2019, 9:20 a.m.